This essay explicates the primary interpretative import of B1: 31-32 in Parmenides poem (On Nature)—lines which have radical implications for the overall argument, and which the traditional arrangement forces into an irreconcilable dilemma. I argue that the “negative” reading of lines 31-32 is preferable, even on the traditional arrangement. This negative reading denies that a third thing is to be taught to the reader by the goddess—a positive account of how the apparent world is to be “acceptably” understood. I then (...) suggest that a rearrangement of the fragments would make more sense overall, while further supporting the “negative” reading as more natural and coherent. In particular, the rearrangement dispels the objection that, “if mortal opinions were not true, why would Parmenides include such a lengthy false account of the apparent world--an account which explicitly denies the conclusions of the earlier section, Truth?”. (shrink)

The primary interpretative challenge for understanding Parmenides’ poem revolves around explaining both the meaning of, and the relationship between, its two primary sections: a) the positively endorsed metaphysical arguments which describe some unified, unchanging, motionless, and eternal “reality”, and b) the ensuing cosmology, which incorporates the very principles explicitly denied in Aletheia. I will refer to this problem as the “A-D Paradox.” I advocate resolving this paradoxical relationship by reading Parmenides’ poem as a ring-composition, and incorporating a modified version of (...) Palmer’s modal interpretation of Aletheia. On my interpretation, Parmenides’ thesis in Aletheia is not a counter-intuitive description of how all the world must truly be, but rather a radical rethinking of divine nature. Understanding Aletheia in this way, the ensuing “cosmology” can be straightforwardly rejected as an exposition of how traditional, mythopoetic accounts have misled mortals in their understanding of divinity. Not only does this interpretative view provide a resolution to the A-D Paradox, it offers a more holistic account of the poem by making the opening lines of introduction integral to understanding Parmenides’ message. By setting forth its own unacceptable fiction, paralleling the elements of the Doxa in a ring-composition, the Proem simultaneously establishes the scope of the ensuing inquiry, and its target. Maintaining Parmenides’ historical position as the “father of metaphysics,” the narrative that he advanced a strictly secular account of all reality is challenged. Instead, Parmenides is best understood as further advancing Xenophanes’ criticisms of traditional religion, an intellectual relationship which the ancient testimonia strongly supports. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic cognitive models. While Conceptual Spaces (...) are revolutionary, they lack an underlying mathematical framework. Several such frameworks have attempted to represent Conceptual Spaces, but by far the most robust is the model developed by Holender. His model utilizes integer linear programming in order to obtain an overall similarity value between observations and concepts that support the formation of hypotheses. This paper will describe a method for building Conceptual Spaces models for threats that utilizes ontologies as a means to provide a clear semantic foundation for this inferencing process; in particular threat ontologies and space domain ontologies are developed and employed in this approach. A space situational awareness use-case is presented involving a kinetic kill scenario and results are shown to assess the performance of this fusion-based inferencing framework. (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This presents several challenges to this data (...) fusion framework. The first is the challenge involved in handling multiple complex terminologies, which is addressed by drawing on a set of Space Domain Ontologies. Another challenge is the complex combinatorics involved when considering all possible feature combinations. This can be mitigated by using integer linear programming optimization that is outlined by the Complex Conceptual Spaces Single Observation mathematical model framework. A third challenge is the complicated physics that is involved in a spacecraft collision that must be addressed to obtain a better understanding of threat assessment. Overcoming these various challenges allows for a quantitative ranking for the potential of a kinetic kill collision across multiple spacecraft pairs. In addition to overcoming these challenges this paper will break down threat assessment into four domains and identify a ranking of threat both for each individual domain and for the four domains combined. Simulation results are shown to verify the developed concepts. (shrink)

Previous work has shown that the Complex Conceptual Spaces − Single Observation Mathematical framework is a useful tool for event characterization. This mathematical framework is developed on the basis of Conceptual Spaces and uses integer linear programming to find the needed similarity values. The work of this paper is focused primarily on space event characterization. In particular, the focus is on the ranking of threats for malicious space events such as a kinetic kill. To make the Conceptual Spaces framework work, (...) the similarity values between the contents of observations on the one hand and the properties of the entities observed on the other needs to be found. This paper shows how to exploit Dempster-Shafer theory to implement a statistical approach for finding these similarities values. This approach will allow a user to identify the uncertainty involved in similarity value data, which can later be propagated through the developed mathematical model in order for the user to know the overall uncertainty in the observation-to-concept mappings needed for space event characterization. (shrink)

There is a basic distinction, in the realm of spatial boundaries, between bona fide boundaries on the one hand, and fiat boundaries on the other. The former are just the physical boundaries of old. The latter are exemplified especially by boundaries induced through human demarcation, for example in the geographic domain. The classical problems connected with the notions of adjacency, contact, separation and division can be resolved in an intuitive way by recognizing this two-sorted ontology of boundaries. Bona fide boundaries (...) yield a notion of contact that is effectively modeled by classical topology; the analogue of contact involving fiat boundaries calls, however, for a different account, based on the intuition that fiat boundaries do not support the open/closed distinction on which classical topology is based. In the presence of this two-sorted ontology it then transpires that mereotopology—topology erected on a mereological basis—is more than a trivial formal variant of classical point-set topology. (shrink)

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

The history of evolution is a history of development from less to more complex organisms. This growth in complexity of organisms goes hand in hand with a concurrent growth in complexity of environments and of organism-environment relations. It is a concern with this latter aspect of evolutionary development that motivates the present paper. We begin by outlining a theory of organism-environment relations. We then show that the theory can be applied to a range of different sorts of cases, both biological (...) and non-biological, in which objects are lodged or housed within specific environments, or niches. Biological science is interested in types—for example in genotypes, phenotypes, and environment types—in regularities that can serve as the basis for the formulation of laws or general principles. Types, however, can exist only through their corresponding tokens. Our theory of token environments is meant to plug this gap and to provide a first step towards a general theory of causally relevant spatial volumes. (shrink)

The concept of niche (setting, context, habitat, environment) has been little studied by ontologists, in spite of its wide application in a variety of disciplines from evolutionary biology to economics. What follows is a first formal theory of this concept, a theory of the relations between objects and their niches. The theory builds upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology. It will be illustrated above all by means of simple biological (...) examples, but the concept of niche should be understood as being, like concepts such as part, boundary, and location, a structural concept that is applicable in principle to a wide range of different domains. (shrink)

Recent work by Peijnenburg, Atkinson, and Herzberg suggests that infinitists who accept a probabilistic construal of justification can overcome significant challenges to their position by attending to mathematical treatments of infinite probabilistic regresses. In this essay, it is argued that care must be taken when assessing the significance of these formal results. Though valuable lessons can be drawn from these mathematical exercises (many of which are not disputed here), the essay argues that it is entirely unclear that the form of (...) infinitism that results meets a basic requirement: namely, providing an account of infinite chains of propositions qua reasons made available to agents. (shrink)

A collaborative article by the Editorial Collective of Social Imaginaries. Investigations into social imaginaries have burgeoned in recent years. From ‘the capitalist imaginary’ to the ‘democratic imaginary’, from the ‘ecological imaginary’ to ‘the global imaginary’ – and beyond – the social imaginaries field has expanded across disciplines and beyond the academy. The recent debates on social imaginaries and potential new imaginaries reveal a recognisable field and paradigm-in-the-making. We argue that Castoriadis, Ricoeur, and Taylor have articulated the most important theoretical frameworks (...) for understanding social imaginaries, although the field as a whole remains heterogeneous. We further argue that the notion of social imaginaries draws on the modern understanding of the imagination as authentically creative. We contend that an elaboration of social imaginaries involves a significant, qualitative shift in the understanding of societies as collectively and politically-instituted formations that are irreducible to inter-subjectivity or systemic logics. After marking out the contours of the field and recounting a philosophical history of the imagination, the essay turns to debates on social imaginaries in more concrete contexts, specifically political-economic imaginaries, the ecological imaginary, multiple modernities and their inter-civilisational encounters. The social imaginaries field imparts powerful messages for the human sciences and wider publics. In particular, social imaginaries hold significant implications for ontological, phenomenological and philosophical anthropological questions; for the cultural, social, and political horizons of contemporary worlds; and for ecological and economic phenomena. The essay concludes with the argument that social imaginaries as a paradigm-in-the-making offers valuable means by which movements towards social change can be elucidated as well providing an open horizon for the critiques of existing social practices. (shrink)

In his latest book, Michael Devitt rejects Chomsky’s mentalist conception of linguistics. The case against Chomsky is based on two principal claims. First, that we can separate the study of linguistic competence from the study of its outputs: only the latter belongs to linguistic inquiry. Second, Chomsky’s account of a speaker’s competence as consisiting in the mental representation of rules of a grammar for his language is mistaken. I shall argue, first, that Devitt fails to make a case for separating (...) the study of outputs from the study of competence, and second, that Devitt mis-characterises Chomsky’s account of competence, and so his objections miss their target. Chomsky’s own views come close to a denial that speaker’s have knowledge of their language. But a satisfactory account of what speakers are able to do will need to ascribe them linguistic knowledge that they use to speak and understand. I shall explore a conception of speaker’s knowledge of language that confirrns Chomsky’s mentalist view of linguistics but which is immune to Devitt’s criticism. (shrink)

We rely on language to know the minds of others, but does language have a role to play in knowing our own minds? To suppose it does is to look for a connection between mastery of a language and the epistemic relation we bear to our inner lives. What could such a connection consist in? To explore this, I shall examine strategies for explaining self-knowledge in terms of the use we make of language to express and report our mental states. (...) Success in these strategies will depend on the view we take of speakers' understanding of the words they use to speak their minds. The key is to avoid circularity in the account of how they know what they mean; for if knowing what one is saying in speaking a language provides a means of knowing one's own mind, it cannot simply be a part of it. I shall look at ways in which we might proceed here, and examine whether the strategy can make room for a genuinely first-person point of view. But first let me try to motivate the problem of self-knowledge. (shrink)

In this paper, we defend Socratic studies as a research programme against several recent attacks, including at least one recently published in Polis. Critics have argued that the study of Socrates, based upon evidence mostly or entirely derived from some set of Plato’s dialogues, is sfounded upon faulty and indefensible historical or hermeneutical technique. We begin by identifying what we believe are the foundational principles of Socratic studies, as the field has been pursued in recent years, and we then show (...) how the research programme that derives from accepting these principles is not defeated by any of the most common recent criticisms of it. Specifically, we argue that challenges to sorting Plato’s dialogues by date, more general challenges to historicist interpretations of Plato’s dialogues, as well as recent literary criticisms of Socratic studies all fail to undermine the research programme. We conclude with some thoughts about how and why Socratic studies has proved itself a valuable and fruitful research programme. (shrink)

Human cognitive acts are directed towards objects extended in space of a wide range of different types. What follows is a new proposal for bringing order into this typological clutter. The theory of spatially extended objects should make room not only for the objects of physics but also for objects at higher levels, including the objects of geography and of related disciplines. It should leave room for different types of boundaries, including both the bona fide boundaries which we find in (...) the physical world and the fiat (or human-demarcation-induced) boundaries with which much of geography has to deal. Two distinct axiomatic theories of boundaries are accordingly presented, and the need for both is examined in some detail. The resultant dual framework is shown to have application above all for our understanding of issues involving contact, division, and separation, issues which have posed serious difficulties for the ontological theories of boundaries that have been proposed hitherto. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

In uttering a sentence we are often take to assert more than its literal meaning - though sometimes we assert less. This phenomenon is taken by many to show that what is said or asserted by a speaker on an occasion is a contextually enriched or developed version of the semantic content of the words uttered. I argue that we can resist this conclusion by recognizing that what we think we are asserting, or take others to assert, involves selective attention (...) to just one of the ways a sentence could be true and neglects others. In most conversations people converge in their selective attention and communication is not impaired. Though in the case of sentences involving predicates of personal taste, people's attention to aspects of what is claimed differs and this can lead to intractable disputes. I offer a diagnosis of such disputes where speakers can disagree about the same claim and both be right. (shrink)

We propose the beginnings of a general theory of environments, of the parts or regions of space in which organisms live and move. We draw on two sources: on the one hand on recent work on the ontology of space; and on the other hand on work by ecological scientists on concepts such as territory, habitat, and niche. An environment is in first approximation a volume of space; it is a specific habitat, location, or site that is suitable or adequate (...) for given purposes (of foraging, resting, hunting, breeding, nesting, grooming) in the life of an organism or group of organisms. This spatial notion of environment can be drawn closer to biological and ecological science by taking account of the pertinent physical attributes realized within given spatial regions. (shrink)

A series of papers on different aspects of practical knowledge by Roderick Chisholm, Rudolf Haller, J. C. Nyiri, Eva Picardi, Joachim Schulte Roger Scruton, Barry Smith and Johan Wrede.

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

In uttering a sentence we are often taken to assert more than its literal meaning — though we sometimes assert less. Robyn Carston and others take this phenomenon to show that what is said or asserted by a speaker on an occasion of utterance is usually a contextuallyenriched version of the semantic content of the sentence. I shall argue that we can resist this conclusion if we recognize that what we think we are asserting, or take others to be asserting, (...) involves selective attention to one of the ways a sentence could be true and neglects others. Most of the time people converge in their selective attention and so communication is not impaired. Though in the case of sentences involving predicates of taste, people’s attention to different aspect of the truth conditions leads to seemingly intractable disputes. I will propose a treatment of such cases on which speakers mean the same by a sentence, assert no more than its semantic content, hold conflicting opinions about its truth-value, and are both right. (shrink)

The new Chomskian orthodoxy denies that our linguistic competence gives us knowledge *of* a language, and that the representations in the language faculty are representations *of* anything. In reply, I have argued that through their intuitions speaker/hearers, (but not their language faculties) have knowledge of language, though not of any externally existing language. In order to count as knowledge, these intuitions must track linguistic facts represented in the language faculty. I defend this idea against the objections Collins has raised to (...) such an account. (shrink)

The critic Cyril Connolly once pointed out that diarists don’t make novelists. He went on to describe the problem for the would-be writer. “Writing for oneself: no public. Writing for others: no privacy” (Cyril Connolly, Journal). This paper addresses Connolly's worry about the public ad private: how can we reconcile the inner and conscious dimension of speech with its outer and public dimension? For if what people mean by their words involves, or consists in, what they have in mind when (...) they speak then how can what someone has in mind — the meaning she attaches to her words — be at the same time publicly accessible to others on the basis of her behaviour? The issue is whether there is a notion of the linguistic meaning of an expression that can do justice to both speakers’ inner experience of comprehension and to what is outwardly available in their public practice. (shrink)

In this paper we argue that Socrates is a cognitivist about emotions, but then ask how the beliefs that constitute emotions can come into being, and why those beliefs seem more resistant to change through rational persuasion than other beliefs.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

In “Toward an Ontology of Commercial Exchange” [11], we proposed human readable definitions for terms that are central to an ontology of commercial exchange. This paper furthers that project in two ways. First, the definitions have been modified to be compatible with the Common Core Ontologies (CCO). CCO is used in a wide variety of domains including the industrial and military domains. Having a commerce ontology compatible with CCO allows data about the exchange of goods relevant to those domains to (...) be tagged with compatible ontologies. Second, we propose preliminary formalizations of these definitions, with the aim of informing the creation of an ontology which can be used to assist in reasoning over businessrelated data. (shrink)

Pojęcie niszy (otoczenia, kontekstu, siedliska, środowiska) nie cieszy się specjalnym zainteresowaniem ontologów, mimo że ma szerokie zastosowanie w rozmaitych dyscyplinach, od biologii ewolucyjnej po ekonomię. Niniejszy artykuł zawiera pierwszą teorię formalną tego pojęcia — teorię relacji pomiędzy przedmiotami a ich niszami. Teoria ta opiera się na istniejącym dorobku mereologii, topologii i teorii lokalizacji przestrzennej, które są narzędziami ontologii formalnej. Jest ona tutaj ilustrowana głównie za pomocą prostych przykładów z biologii, ale pojęcie niszy należy rozumieć — podobnie jak pojęcia części, granicy (...) i położenia — jako pojęcie strukturalne, znajdujące zastosowanie w obszernym zakresie różnych dziedzin. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

Plato is often acknowledged as the first philosophical critic of democracy and his Republic is regularly taken as a paradigm of an anti-democratic work. While it is true that Plato objected to much about the democracy of his own time, Plato’s political theorizing also reveals an interest in improving democratic institutions. This chapter explores three themes in Plato’s thinking about democracy: firstly, Plato's insistence that rulers should be knowledgeable and his claim that most people are politically incompetent (§1); secondly, Plato's (...) criticisms of oratory and the corrupting effects of public rhetoric (§2); thirdly, Plato's use of democratic institutions in the Laws (§3). Once we appreciate these different evaluations of democratic practices, we can see that Plato was not simply ‘anti-democratic’ or ‘pro-democratic’ but thought some democratic practices should be abandoned, some reformed, and some adopted. (shrink)

Commentators have often been puzzled by the structure of the _Symposium_; in particular, it is unclear what the relationship is between Socrates’ speech and that of the other symposiasts. This chapter seeks to make a contribution to that debate by highlighting parallels between the first four speeches of the _Symposium_ and the goals of the early education in the Republic. In both dialogues, I contend, we see Plato concerned with educating people through (a) activating and cultivating spirited motivations, (b) becoming (...) lawful and taking virtue as a goal, (c) harmonizing the opposing forces in their soul, and (d) minimizing the appetites and making them orderly. While these are familiar points from the moral education of the Republic, I argue that they also map onto the first four speeches of the _Symposium_ respectively. Because in the _Republic_ this moral education is necessary to make progress on the epistemic ascent, we can speculate that there is a similar point to be made in the _Symposium_ – without first training our character adequately, we will not be able to climb the ladder of love. While the positive effects of Eros described in the early speeches of the _Symposium_ are only imitations of the ideal education regime of Kallipolis, they nevertheless improve one’s character in such a way that better prepares the soul for philosophy. Finally, I argue that the importance of this moral education is dramatized at the end of the _Symposium_ through Agathon’s amicable refutation by Socrates on the one hand, and the drunken entrance of Alcibiades on the other. Agathon shows potential for philosophy whereas Alcibiades is the exemplar of what happens when somebody comes to philosophy without a harmonized soul. (shrink)

The parceling of land into real estate is more than a simple geometrical affair. Real estate is a historical product of interaction between human beings, political, legal and economic institutions, and the physical environment. And while many authors, from Jeremy Bentham to Hernando de Soto, have drawn attention to the ontological (metaphysical) aspect of property in general, no comprehensive analysis of landed property has been attempted. The paper presents such an analysis and shows how landed property differs from other (...) types of property in a way which implies a special role for political and economic philosophy of property rights in land. This is the Chinese translation of "The Metaphysics of Real Estate", Topoi, 20: 2 (September 2001), 161–172. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...) making computers understand medical natural language. (shrink)

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a bank's computers, however, the formula fails, (...) because these are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account. (shrink)

Polish translation of "John Searle: From Speech Acts to Social Reality", -/- We provide an overview of Searle's contributions to speech act theory and the ontology of social reality, focusing on his theory of constitutive rules. In early versions of this theory, Searle proposed that all such rules have the form 'X counts as Y in context C' formula – as for example when Barack Obama (X) counts as President of the United States (Y) in the context of US political (...) affairs. Crucially, the X and the Y terms are here identical. A problem arises for this theory for cases involving 'free-standing Y terms', as for example in the case of money in a computerized bank account. Here there is no physical X to which a status function might be attached. We conclude by arguing that Searle's response to this problem creates difficulties for his naturalistic framework. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

We have a variety of different ways of dividing up, classifying, mapping, sorting and listing the objects in reality. The theory of granular partitions presented here seeks to provide a general and unified basis for understanding such phenomena in formal terms that is more realistic than existing alternatives. Our theory has two orthogonal parts: the first is a theory of classification; it provides an account of partitions as cells and subcells; the second is a theory of reference or intentionality; it (...) provides an account of how cells and subcells relate to objects in reality. We define a notion of well-formedness for partitions, and we give an account of what it means for a partition to project onto objects in reality. We continue by classifying partitions along three axes: (a) in terms of the degree of correspondence between partition cells and objects in reality; (b) in terms of the degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) in terms of the degree of completeness with which a partition represents this domain. (shrink)

In 1890 Christian von Ehrenfels published his classic paper "Über 'Gestaltqualitäten'", the first systematic investigation of the philosophy and psychology of Gestalt. Ehrenfels thereby issued an important challenge to the psychological atomism that was still predominant in his day. His paper not only exerted a powerful influence on the philosophy of the Meinong school, it also marked the beginning of the Gestalt tradition in psychology, later associated with the work of Wertheimer, Köhler and Koffka in Berlin. Includes papers by C. (...) Von Ehrenfels, Kurt Grelling and Paul Oppenheim and contributions by K. Mulligan, P.M. Simons and Barry Smith. (shrink)

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney (...) and skin. (shrink)

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: -/- The main aim of this review will be to assess the effects of changing practitioner empathy or patient expectations for all conditions. The main objective is to conduct a systematic review of randomised trials where the intervention involves manipulating either (a) practitioner empathy or (b) patient expectations, or (c) both.

This is a revised version of the introductory essay in C. Eschenbach, C. Habel and B. Smith (eds.), Topological Foundations of Cognitive Science, Hamburg: Graduiertenkolleg Kognitionswissenschaft, 1994, the text of a talk delivered at the First International Summer Institute in Cognitive Science in Buffalo in July 1994.

In order to graduate, Florida's high school students by law must learn that Communism is evil, dangerous, and fallacious. All students must learn that the U.S. produces the highest standard of living and more freedom than any other economic system on earth. State universities in Florida are creating a curriculum to implement the Americanism versus Communism Act of 1961 and the Free Enterprise and Consumer Education Act of 1975. ;The Florida Department of Education says that ideology, noncritical thinking, is superior (...) to critical thinking and that the superiority of the U.S. political economy and the dignity of the individual rest in part on peoples' being able to express themselves freely. ;Florida's A.V.C. and F.E.C.E.A. proponents have a special way of convincing audiences that they will develop loyalty while at the same time imposing a set of ideas not open to question. ;This work argues that, intentionally or not, Florida's legislature and Department of Education have set up an official ideology and the mechanism to purvey it. This ideological approach defeats the aim of comparing systems objectively. While the stated aim is to promote critical thinking, the D.O.E.'s special philosophy underscoring words like "democracy" results in indoctrinating students with a questionable description of the U.S. system. (shrink)